1J31

Crystal Structure of Hypothetical Protein PH0642 from Pyrococcus horikoshii

• PDB DOI: https://doi.org/10.2210/pdb1J31/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Pyrococcus horikoshii OT3
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-01-16 Released: 2004-03-09 
• Deposition Author(s): Sakai, N., Tajika, Y., Yao, M., Watanabe, N., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.194 
• R-Value Work: 0.166 
• R-Value Observed: 0.166 

Literature

Crystal structure of hypothetical protein PH0642 from Pyrococcus horikoshii at 1.6A resolution.

Sakai, N., Tajika, Y., Yao, M., Watanabe, N., Tanaka, I.

(2004) Proteins 57: 869-873

• PubMed: 15390259 
• DOI: https://doi.org/10.1002/prot.20259
• Primary Citation of Related Structures:  
  1J31

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Organizational Affiliation: 

Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 120.93 kDa 
• Atom Count: 9,070 
• Modelled Residue Count: 1,048 
• Deposited Residue Count: 1,048 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein PH0642	A, B, C, D	262	Pyrococcus horikoshii OT3	Mutation(s): 7  Gene Names: PH0642
UniProt
Find proteins for O58376 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58376  Go to UniProtKB:  O58376

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	E [auth A], F [auth B], G [auth C], H [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.194 
• R-Value Work: 0.166 
• R-Value Observed: 0.166 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.037	α = 90
b = 89.021	β = 96.15
c = 77.871	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-09 
Deposition Author(s): Sakai, N., Tajika, Y., Yao, M., Watanabe, N., Tanaka, I.

Revision History  

• Version 1.0: 2004-03-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Structure summary